X-group (possible homology)

227 DNA clamp

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Ligands and drugs

3,396

Member domains

596

with ligand contacts (≤ 4 Å)

17.6% of members

549

with DrugDomain annotations

16.2% of members

257

with a DrugBank compound

7.6% of members

Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.

Chemical profile

ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.

Proteins with classified ligands

Superclasses bound (of 23)

7.6

Superclasses per 20 proteins

narrower than 51% of the 256 X-groups with enough proteins to compare (median 7.6)

The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.

Superclass	Proteins	Expected	Ratio	Significance
Homogeneous non-metal compounds	15	6.2	2.44×	q = 7.9e-4
Organic oxygen compounds	9	5.7	1.58×	q = 0.21
Homogeneous metal compounds	14	14.0	1.00×	q = 1.00
Nucleosides, nucleotides, and analogues	0	7.9	0	q = 5.5e-4
Hydrocarbons	1	0.2	5.01×	not tested
Organosulfur compounds	2	0.6	3.40×	not tested
Benzenoids	4	2.1	1.91×	not tested
Organic acids and derivatives	6	4.4	1.36×	not tested
Organoheterocyclic compounds	4	4.4	0.91×	not tested

enriched (q < 0.05)depleted (q < 0.05)not significantnot tested (expected < 5)

Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.

DrugBank compounds

DrugBank	PDB ligand	Name	Domains
DB00120	PHE	Phenylalanine	4
DB00125	ARG	Arginine	4
DB00149	LEU	Leucine	4
DB00738	PNT	Pentamidine	4
DB00861	1FL	Diflunisal	4
DB02967	NEQ	N-Ethylmaleimide	4
DB06998	322	[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid	4
DB00142	GLU	Glutamic acid	2
DB00156	THR	Threonine	2
DB00279	T3	Liothyronine	2
DB00945	—	Acetylsalicylic acid	2
DB00963	27R	Bromfenac	2
DB02159	PGR	(R)-Propylene glycol	2
DB03100	6NI	6-Nitroindazole	2
DB07108	4FC	4'-FLUORO-1,1'-BIPHENYL-4-CARBOXYLIC ACID	2
DB02078	PG5	Triglyme	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	105
CL	CHLORIDE ION	74
NAmetal	SODIUM ION	36
BR	BROMIDE ION	18
ZNmetal	ZINC ION	16
ACE	ACETYL GROUP	10
MGmetal	MAGNESIUM ION	10
IOD	IODIDE ION	6
NEQ	N-ETHYLMALEIMIDE	6
Kmetal	POTASSIUM ION	5
0LA	(2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid	4
1FL	5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID	4
2HO	3,4-difluorobenzamide	4
2HQ	5-chloro-1H-indole-2,3-dione	4
2VD	(2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid	4
2VF	(2R)-9-(2-amino-2-oxoethyl)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid	4
2VG	(2R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid	4
2VM	(2R)-6-bromo-9-(2-{[(1S)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid	4
322	[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid	4
743	(1R,5R)-5-{(1Z)-N-[(4'-fluorobiphenyl-4-yl)methoxy]butanimidoyl}-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile	4